Rise and Fall of Trilobites: Fossil Records Over Time

Exploring the dramatic rise and fall of one of Earth’s most successful early arthropod groups

30DayChartChallenge

Data Visualization

R Programming

2025

Visualizing 250 million years of trilobite fossil records from the Paleobiology Database, showing how these ancient arthropods dominated the Ordovician seas before declining after major extinction events.

Published

April 21, 2025

Figure 1: Line graph showing the rise and fall of trilobite fossils over time (540-250 million years ago). The data peaks in the Ordovician period around 480-450 Ma, then sharply declines after the Ordovician Extinction (444 Ma), continues at lower levels through the Silurian period, and diminishes further after the Devonian Extinction (372 Ma).

Steps to Create this Graphic

1. Load Packages & Setup

Show code

## 1. LOAD PACKAGES & SETUP ----
suppressPackageStartupMessages({
pacman::p_load(
  tidyverse,      # Easily Install and Load the 'Tidyverse'
  ggtext,         # Improved Text Rendering Support for 'ggplot2'
  showtext,       # Using Fonts More Easily in R Graphs
  janitor,        # Simple Tools for Examining and Cleaning Dirty Data
  skimr,          # Compact and Flexible Summaries of Data
  scales,         # Scale Functions for Visualization
  lubridate,      # Make Dealing with Dates a Little Easier
  paleobioDB,     # Download and Process Data from the Paleobiology Database # Download and Process Data from the Paleobiology Database
  ggrepel,        # Automatically Position Non-Overlapping Text Labels with 'ggplot2' 
  camcorder       # Record Your Plot History
  )
})

### |- figure size ----
gg_record(
    dir    = here::here("temp_plots"),
    device = "png",
    width  = 8,
    height = 8,
    units  = "in",
    dpi    = 320
)

# Source utility functions
suppressMessages(source(here::here("R/utils/fonts.R")))
source(here::here("R/utils/social_icons.R"))
source(here::here("R/utils/image_utils.R"))
source(here::here("R/themes/base_theme.R"))

2. Read in the Data

Show code

# Search for fossil occurrences of trilobites 
trilobites <- pbdb_occurrences(
  base_name = "Trilobita", 
  show = c("time", "coords", "phylo"), 
  limit = "all"
  )

3. Examine the Data

Show code

glimpse(trilobites)
skim(trilobites)

4. Tidy Data

Show code

### |- Tidy ----
trilo_time_binned <- trilobites |>
  filter(!is.na(eag), !is.na(lag)) |>      
  mutate(
    mid_ma = (eag + lag) / 2,
    bin_5ma = floor(mid_ma / 5) * 5 ,
    bin_10ma = floor(mid_ma / 10) * 10
  ) |>
  count(bin_5ma) |>
  arrange(desc(bin_5ma))

5. Visualization Parameters

Show code

### |-  plot aesthetics ----
colors <- get_theme_colors(
  palette = c(
    "#D95F02" ,
    "gray20"
  )
)

### |-  titles and caption ----
# text
title_text    <- str_wrap("Rise and Fall of Trilobites: Fossil Records Over Time",
                          width = 55) 

subtitle_text <- str_wrap("Exploring the dramatic rise and fall of one of Earth's most successful early arthropod groups",
                          width = 85)

caption_text <- create_dcc_caption(
  dcc_year = 2025,
  dcc_day = 21,
  source_text =  "{ paleobioDB } R package" 
)

### |-  fonts ----
setup_fonts()
fonts <- get_font_families()

### |-  plot theme ----

# Start with base theme
base_theme <- create_base_theme(colors)

# Add weekly-specific theme elements
weekly_theme <- extend_weekly_theme(
  base_theme,
  theme(

    # Axis elements
    axis.title.y = element_text(color = colors$text, size = rel(0.8), margin = margin(r = 10)),
    axis.text = element_text(color = colors$text, size = rel(0.7)),
    axis.line.x = element_line(color = "black"),
    axis.ticks.x = element_line(color = "black"),

    # Grid elements
    panel.grid.minor = element_blank(),
    panel.grid.major.x = element_blank(),
    panel.grid.major.y = element_line(color = "gray92"),

    # Legend elements
    legend.position = "plot",
    legend.title = element_blank(),
    legend.text = element_text(family = fonts$text, size = rel(0.7)),
    
    # Facet elements
    strip.background = element_rect(fill = "gray90", color = NA),
    strip.text = element_text(face = "bold", size = rel(1), margin = margin(10, 0, 10, 0)),
    
    # Plot margins 
    plot.margin = margin(t = 10, r = 20, b = 10, l = 20),
  )
)

# Set theme
theme_set(weekly_theme)

6. Plot

Show code

### |-  Plot ----
p <- ggplot(trilo_time_binned, aes(x = bin_5ma, y = n)) +
  # Geoms
  geom_area(fill = colors$palette[1], alpha = 0.2) +
  geom_line(color = colors$palette[1], linewidth = 1.5) +
  geom_point(color = colors$palette[1], size = 1.5, alpha = 0.7) +
  geom_vline(xintercept = 444, linetype = "dashed", color = colors$palette[2], alpha = 0.4, linewidth = 0.7) +
  geom_vline(xintercept = 372, linetype = "dashed", color = colors$palette[2], alpha = 0.4, linewidth = 0.7) +
  # Annotate
  annotate("text",
    x = 444, y = 5000,
    label = "Ordovician Extinction",
    color = colors$palette[2], hjust = 1.1, size = 3.5
  ) +
  annotate("text",
    x = 372, y = 5000,
    label = "Devonian Extinction",
    color = colors$palette[2], hjust = 1.1, size = 3.5
  ) +
  annotate("text",
    x = 475, y = -283.8,
    label = "Ordovician", fontface = "italic", size = 4
  ) +
  annotate("text",
    x = 425, y = -283.8,
    label = "Silurian", fontface = "italic", size = 4
  ) +
  annotate("text",
    x = 390, y = -283.8,
    label = "Devonian", fontface = "italic", size = 4
  ) +
  # Scales
  scale_x_reverse(
    limits = c(520, 250),
    breaks = seq(500, 250, by = -50),
    minor_breaks = seq(500, 250, by = -10)
  ) +
  scale_y_continuous(
    limits = c(-max(trilo_time_binned$n) * 0.1, max(trilo_time_binned$n) * 1.1),
    expand = c(0, 0)
  ) +
  # Labs
  labs(
    title = title_text,
    subtitle = subtitle_text,
    caption = caption_text,
    x = "Millions of Years Ago (Ma)",
    y = "Number of Recorded Fossil Occurrences",
  ) +
  # Theme
  theme(
    plot.title = element_text(
      size = rel(1.8),
      family = fonts$title,
      face = "bold",
      color = colors$title,
      margin = margin(t = 5, b = 5)
    ),
    plot.subtitle = element_text(
      size = rel(0.85),
      family = fonts$subtitle,
      color = colors$subtitle,
      lineheight = 1.2,
      margin = margin(t = 5, b = 15)
    ),
    plot.caption = element_markdown(
      size = rel(0.6),
      family = fonts$caption,
      color = colors$caption,
      lineheight = 0.65,
      hjust = 0.5,
      halign = 0.5,
      margin = margin(t = 10, b = 5)
    ),
  )

7. Save

Show code

### |-  plot image ----  

save_plot(
  p, 
  type = "30daychartchallenge", 
  year = 2025, 
  day = 21, 
  width = 8, 
  height = 8
  )

8. Session Info

Expand for Session Info

R version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8 
[2] LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] here_1.0.1       camcorder_0.1.0  ggrepel_0.9.6    paleobioDB_1.0.0
 [5] scales_1.3.0     skimr_2.1.5      janitor_2.2.0    showtext_0.9-7  
 [9] showtextdb_3.0   sysfonts_0.8.9   ggtext_0.1.2     lubridate_1.9.3 
[13] forcats_1.0.0    stringr_1.5.1    dplyr_1.1.4      purrr_1.0.2     
[17] readr_2.1.5      tidyr_1.3.1      tibble_3.2.1     ggplot2_3.5.1   
[21] tidyverse_2.0.0 

loaded via a namespace (and not attached):
 [1] gtable_0.3.6      rjson_0.2.23      xfun_0.49         htmlwidgets_1.6.4
 [5] tzdb_0.4.0        vctrs_0.6.5       tools_4.4.0       generics_0.1.3   
 [9] curl_6.0.0        gifski_1.32.0-1   fansi_1.0.6       pacman_0.5.1     
[13] pkgconfig_2.0.3   lifecycle_1.0.4   farver_2.1.2      compiler_4.4.0   
[17] textshaping_0.4.0 munsell_0.5.1     terra_1.7-83      repr_1.1.7       
[21] codetools_0.2-20  snakecase_0.11.1  htmltools_0.5.8.1 yaml_2.3.10      
[25] pillar_1.9.0      magick_2.8.5      commonmark_1.9.2  gtools_3.9.5     
[29] tidyselect_1.2.1  digest_0.6.37     stringi_1.8.4     labeling_0.4.3   
[33] rsvg_2.6.1        rprojroot_2.0.4   fastmap_1.2.0     grid_4.4.0       
[37] colorspace_2.1-1  cli_3.6.3         magrittr_2.0.3    base64enc_0.1-3  
[41] utf8_1.2.4        withr_3.0.2       timechange_0.3.0  rmarkdown_2.29   
[45] ragg_1.3.3        hms_1.1.3         evaluate_1.0.1    knitr_1.49       
[49] markdown_1.13     rlang_1.1.4       gridtext_0.1.5    Rcpp_1.0.13-1    
[53] glue_1.8.0        xml2_1.3.6        renv_1.0.3        svglite_2.1.3    
[57] rstudioapi_0.17.1 jsonlite_1.8.9    R6_2.5.1          systemfonts_1.1.0

9. GitHub Repository

Expand for GitHub Repo

The complete code for this analysis is available in 30dcc_2025_21.qmd.

For the full repository, click here.

10. References

Expand for References

Data Sources:
- Paleobiology Database { paleobioDB } indicator = Trilobita)

--- title: "Rise and Fall of Trilobites: Fossil Records Over Time" subtitle: "Exploring the dramatic rise and fall of one of Earth's most successful early arthropod groups" description: "Visualizing 250 million years of trilobite fossil records from the Paleobiology Database, showing how these ancient arthropods dominated the Ordovician seas before declining after major extinction events." date: "2025-04-21" categories: ["30DayChartChallenge", "Data Visualization", "R Programming", "2025"] tags: [ "paleontology", "trilobites", "extinction events", "paleobioDB", "fossil records", "timeseries", "ggplot2", "evolutionary history", "Ordovician", "Silurian", "Devonian" ] image: "thumbnails/30dcc_2025_21.png" format: html: toc: true toc-depth: 5 code-link: true code-fold: true code-tools: true code-summary: "Show code" self-contained: true theme: light: [flatly, assets/styling/custom_styles.scss] dark: [darkly, assets/styling/custom_styles_dark.scss] editor_options: chunk_output_type: inline execute: freeze: true cache: true error: false message: false warning: false eval: true # filters: # - social-share # share: # permalink: "https://stevenponce.netlify.app/data_visualizations/30DayChartChallenge/2025/30dcc_2025_21.html" # description: "Day 21 of #30DayChartChallenge: Exploring trilobite fossil records over 250 million years, revealing their rise during the Ordovician and decline following major extinction events." # twitter: true # linkedin: true # email: true # facebook: false # reddit: false # stumble: false # tumblr: false # mastodon: true # bsky: true --- ![Line graph showing the rise and fall of trilobite fossils over time (540-250 million years ago). The data peaks in the Ordovician period around 480-450 Ma, then sharply declines after the Ordovician Extinction (444 Ma), continues at lower levels through the Silurian period, and diminishes further after the Devonian Extinction (372 Ma). ](30dcc_2025_21.png){#fig-1} ### <mark> **Steps to Create this Graphic** </mark> #### 1. Load Packages & Setup ```{r} #| label: load #| warning: false #| message: false #| results: "hide" ## 1. LOAD PACKAGES & SETUP ---- suppressPackageStartupMessages({ pacman::p_load( tidyverse, # Easily Install and Load the 'Tidyverse' ggtext, # Improved Text Rendering Support for 'ggplot2' showtext, # Using Fonts More Easily in R Graphs janitor, # Simple Tools for Examining and Cleaning Dirty Data skimr, # Compact and Flexible Summaries of Data scales, # Scale Functions for Visualization lubridate, # Make Dealing with Dates a Little Easier paleobioDB, # Download and Process Data from the Paleobiology Database # Download and Process Data from the Paleobiology Database ggrepel, # Automatically Position Non-Overlapping Text Labels with 'ggplot2' camcorder # Record Your Plot History ) }) ### |- figure size ---- gg_record( dir = here::here("temp_plots"), device = "png", width = 8, height = 8, units = "in", dpi = 320 ) # Source utility functions suppressMessages(source(here::here("R/utils/fonts.R"))) source(here::here("R/utils/social_icons.R")) source(here::here("R/utils/image_utils.R")) source(here::here("R/themes/base_theme.R")) ``` #### 2. Read in the Data ```{r} #| label: read #| include: true #| eval: true #| warning: false # Search for fossil occurrences of trilobites trilobites <- pbdb_occurrences( base_name = "Trilobita", show = c("time", "coords", "phylo"), limit = "all" ) ``` #### 3. Examine the Data ```{r} #| label: examine #| include: true #| eval: true #| results: 'hide' #| warning: false glimpse(trilobites) skim(trilobites) ``` #### 4. Tidy Data ```{r} #| label: tidy #| warning: false ### |- Tidy ---- trilo_time_binned <- trilobites |> filter(!is.na(eag), !is.na(lag)) |> mutate( mid_ma = (eag + lag) / 2, bin_5ma = floor(mid_ma / 5) * 5 , bin_10ma = floor(mid_ma / 10) * 10 ) |> count(bin_5ma) |> arrange(desc(bin_5ma)) ``` #### 5. Visualization Parameters ```{r} #| label: params #| include: true #| warning: false ### |- plot aesthetics ---- colors <- get_theme_colors( palette = c( "#D95F02" , "gray20" ) ) ### |- titles and caption ---- # text title_text <- str_wrap("Rise and Fall of Trilobites: Fossil Records Over Time", width = 55) subtitle_text <- str_wrap("Exploring the dramatic rise and fall of one of Earth's most successful early arthropod groups", width = 85) caption_text <- create_dcc_caption( dcc_year = 2025, dcc_day = 21, source_text = "{ paleobioDB } R package" ) ### |- fonts ---- setup_fonts() fonts <- get_font_families() ### |- plot theme ---- # Start with base theme base_theme <- create_base_theme(colors) # Add weekly-specific theme elements weekly_theme <- extend_weekly_theme( base_theme, theme( # Axis elements axis.title.y = element_text(color = colors$text, size = rel(0.8), margin = margin(r = 10)), axis.text = element_text(color = colors$text, size = rel(0.7)), axis.line.x = element_line(color = "black"), axis.ticks.x = element_line(color = "black"), # Grid elements panel.grid.minor = element_blank(), panel.grid.major.x = element_blank(), panel.grid.major.y = element_line(color = "gray92"), # Legend elements legend.position = "plot", legend.title = element_blank(), legend.text = element_text(family = fonts$text, size = rel(0.7)), # Facet elements strip.background = element_rect(fill = "gray90", color = NA), strip.text = element_text(face = "bold", size = rel(1), margin = margin(10, 0, 10, 0)), # Plot margins plot.margin = margin(t = 10, r = 20, b = 10, l = 20), ) ) # Set theme theme_set(weekly_theme) ``` #### 6. Plot ```{r} #| label: plot #| warning: false ### |- Plot ---- p <- ggplot(trilo_time_binned, aes(x = bin_5ma, y = n)) + # Geoms geom_area(fill = colors$palette[1], alpha = 0.2) + geom_line(color = colors$palette[1], linewidth = 1.5) + geom_point(color = colors$palette[1], size = 1.5, alpha = 0.7) + geom_vline(xintercept = 444, linetype = "dashed", color = colors$palette[2], alpha = 0.4, linewidth = 0.7) + geom_vline(xintercept = 372, linetype = "dashed", color = colors$palette[2], alpha = 0.4, linewidth = 0.7) + # Annotate annotate("text", x = 444, y = 5000, label = "Ordovician Extinction", color = colors$palette[2], hjust = 1.1, size = 3.5 ) + annotate("text", x = 372, y = 5000, label = "Devonian Extinction", color = colors$palette[2], hjust = 1.1, size = 3.5 ) + annotate("text", x = 475, y = -283.8, label = "Ordovician", fontface = "italic", size = 4 ) + annotate("text", x = 425, y = -283.8, label = "Silurian", fontface = "italic", size = 4 ) + annotate("text", x = 390, y = -283.8, label = "Devonian", fontface = "italic", size = 4 ) + # Scales scale_x_reverse( limits = c(520, 250), breaks = seq(500, 250, by = -50), minor_breaks = seq(500, 250, by = -10) ) + scale_y_continuous( limits = c(-max(trilo_time_binned$n) * 0.1, max(trilo_time_binned$n) * 1.1), expand = c(0, 0) ) + # Labs labs( title = title_text, subtitle = subtitle_text, caption = caption_text, x = "Millions of Years Ago (Ma)", y = "Number of Recorded Fossil Occurrences", ) + # Theme theme( plot.title = element_text( size = rel(1.8), family = fonts$title, face = "bold", color = colors$title, margin = margin(t = 5, b = 5) ), plot.subtitle = element_text( size = rel(0.85), family = fonts$subtitle, color = colors$subtitle, lineheight = 1.2, margin = margin(t = 5, b = 15) ), plot.caption = element_markdown( size = rel(0.6), family = fonts$caption, color = colors$caption, lineheight = 0.65, hjust = 0.5, halign = 0.5, margin = margin(t = 10, b = 5) ), ) ``` #### 7. Save ```{r} #| label: save #| warning: false ### |- plot image ---- save_plot( p, type = "30daychartchallenge", year = 2025, day = 21, width = 8, height = 8 ) ``` #### 8. Session Info ::: {.callout-tip collapse="true"} ##### Expand for Session Info ```{r, echo = FALSE} #| eval: true #| warning: false sessionInfo() ``` ::: #### 9. GitHub Repository ::: {.callout-tip collapse="true"} ##### Expand for GitHub Repo The complete code for this analysis is available in [`30dcc_2025_21.qmd`](https://github.com/poncest/personal-website/blob/master/data_visualizations/TidyTuesday/2025/30dcc_2025_21.qmd). For the full repository, [click here](https://github.com/poncest/personal-website/). ::: #### 10. References ::: {.callout-tip collapse="true"} ##### Expand for References 1. Data Sources: - Paleobiology Database { paleobioDB } [indicator = Trilobita)](https://github.com/ropensci/paleobioDB) :::